# Machine learning-based evaluation of risk factors for carbapenem-resistant Klebsiella pneumoniae dissemination in neonatal units

## TL;DR

The study uses machine learning to track how carbapenem-resistant Klebsiella pneumoniae spreads in neonatal units, identifying key risk factors like clonal outbreaks and plasmid dynamics.

## Contribution

The novel use of machine learning to analyze CRKP transmission in NICUs reveals new insights into clonal dissemination, healthcare group interactions, and plasmid persistence.

## Key findings

- Three major clonal outbreaks involving ST14 and ST433 strains were identified, emphasizing clonal dissemination in NICUs.
- Healthcare groups were found to mediate short-term transmission, with over 80% of infection clusters involving patients from the same group.
- Plasmids were linked to long-term CRKP persistence, with shifts in plasmid prevalence corresponding to outbreak periods.

## Abstract

Healthcare-associated infections (HAIs), particularly in neonatal intensive
care units (NICUs), pose significant challenges due to neonates’
vulnerability and the rapid infection spread. However, risk factors
facilitating pathogen persistence and dissemination have not been
comprehensively investigated. This study aims to track HAI transmission
pathways in NICUs and identify key risk factors contributing to the
persistence and spread of carbapenem-resistant Klebsiella
pneumoniae (CRKP). We analyzed CRKP epidemiology and population
dynamics in neonatal patients at a pediatric hospital in China over 8 years.
Random forest models identified primary risk factors for CRKP persistence
and outbreaks, focusing on clonal spread, healthcare groups (HGs), and
plasmid dynamics. Three major clonal outbreaks involving ST14 and ST433
strains were identified, highlighting the critical role of clonal
dissemination in NICUs. Complex transmission patterns, characterized by
periods of dormancy and resurgence, suggest the existence of underlying
reservoirs. HGs were implicated in the short-term transmission of CRKP, with
>80% of infection clusters involving patients from the same HG.
Plasmids emerged as critical factors in the long-term persistence of CRKP,
with shifts in plasmid prevalence corresponding to outbreak periods. This
study advances our understanding of CRKP transmission dynamics in NICUs,
highlighting the multifaceted roles of clonal dissemination, HGs, and
plasmid-mediated persistence. Our findings emphasize the need for enhanced
infection control measures targeting both intra- and inter-group
transmissions and plasmid surveillance.

This study provides a detailed analysis of carbapenem-resistant
Klebsiella pneumoniae (CRKP) transmission dynamics
in neonatal intensive care units (NICUs) over eight years, utilizing 64
isolates and applying machine learning to identify risk factors
associated with persistence and spread. Through phylogenetic analyses,
we uncovered three clonal outbreaks and linked healthcare group (HG)
interactions, bacterial genotypes, and plasmid prevalence to short- and
long-term CRKP transmission. We identified that HGs are primary
mediators of rapid, short-term transmission, while specific plasmids
play an extended role in maintaining CRKP presence across multiple
patient cohorts and bacterial strains. This finding suggests the
existence of latent reservoirs or periodic reintroductions from external
sources, thus reshaping the understanding of NICU-associated pathogen
transmission and persistence.